New and revised gene ontology biological process terms describe multiorganism interactions critical for understanding microbial pathogenesis and sequences of concern

• Published in: Journal of biomedical semantics Vol. 16; no. 1; pp. 4 - 9
• Main Authors: Godbold, Gene, Proescher, Jody, Gaudet, Pascale
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 21.03.2025; BioMed Central; BMC
• Subjects: Animals; Biological activity; Cell cycle; Controlled vocabularies; Dual use research of concern; Exploitation; Gene Ontology; Genetic research; Host-Pathogen Interactions - genetics; Humans; Infectious diseases; Life sciences; Methods; Microbial genetics; Microbial pathogenesis; Microorganisms; Nucleic acids; Nucleotides; Ontologies; Ontology; Pathogenesis; Pathogenicity; Pathogens; Physiological aspects; Screening; Sequences; Synthetic nucleotide screening; Terminology as Topic; Toxicity; Toxins; Virulence; Web Ontology Language-OWL; United States; United States > US; Synthetic nucleotide screening; Ontologies; Dual use research of concern; Infectious diseases; Controlled vocabularies; Microbial pathogenesis
• ISSN: 2041-1480; 2041-1480
• DOI: 10.1186/s13326-025-00323-8

There is a new framework from the United States government for screening synthetic nucleic acids. Beginning in October of 2026, it calls for the screening of sequences 50 nucleotides or greater in length that are known to contribute to pathogenicity or toxicity for humans, regardless of the taxa from which it originates. Distinguishing sequences that encode pathogenic and toxic functions from those that lack them is not simple. Our project scope was to discern, describe, and catalog sequences involved in microbial pathogenesis from the scientific literature. We recognize a need for better terminology to designate pathogenic functions that are relevant across the entire range of existing parasites. We canvassed publications investigating microbial pathogens of humans, other animals, and some plants to collect thousands of sequences that enable the exploitation of hosts. We compared sequences to each other, grouping them according to what host biological processes they subvert and the consequence(s) for the host. We developed terms to capture many of the varied pathogenic functions for sequences employed by parasitic microbes for host exploitation and applied these terms in a systematic manner to our dataset of sequences. The enhanced and expanded terms enable a quick and pertinent evaluation of a sequence's ability to endow a microbe with pathogenic function when they are appropriately applied to relevant sequences. This will allow providers of synthetic nucleic acids to rapidly assess sequences ordered by their customers for pathogenic capacity. This will help fulfill the new US government guidance.